Emails do not retain text formats when site uses WYSIWYG or modifies default input format

Both the inbound and outbound email do not retain linebreaks and formats in the support module when the site uses a WYSIWYG or modifies default input format. On outbound emails this is because the check_plain() function is not passed the input format of the node or comment. On inbound emails the support modules assumes HTML format and strips tags. For both cases the text looses line breaks and other possible formatting which makes it very difficult to read. e.g

Original:

Here is some text.
There is a a newline here.

Now a double line break.

Munged:

Here is some text. There is a a newline here. Now a double line break.

This may also interfer with additional modules that send HTML + plain text emails. I can get even worse when replies are created on the Drupal site using a HTML format and all the HTML is stripped.